While on a reconnaissance mission of star systems near the Bajoran wormhole, O'Brien and Sisko discover human life signs on an uncharted planet. Beaming to the surface, they suddenly discover that a duonetic energy field has disabled all of their electronic devices. They meet Joseph and Vinod, part of a group of colonists who became stranded ten years ago in a similar fashion. Sisko reassures them and the other colonists that someone will find the runabout in orbit, the leader of the colonists and Vinod's mother, Alixus, announces that she is proud of what they have accomplished and intends to stay.

As Kira and Dax search for Sisko and O'Brien, Sisko discovers that prior to becoming stranded, Alixus was a philosopher and critic of Humans' dependence on technology. Meanwhile, O'Brien searches for something he could use to contact the runabout, but Joseph admits that the colonists threw away all of their technological devices. Although he was the last "convert" to accept Alixus's philosophy, Joseph is pleased with what he and the others have accomplished.

One of the colonists, Meg, is dying and could potentially be cured with the runabout's medical supplies, but when Sisko and O'Brien discuss possible methods of contacting the runabout, Alixus takes Sisko outside. She tells him that such talk is not productive; he disagrees and she tells him that he will eventually have to do things her way. Leaving him, Alixus suggests Sisko take off his uniform, as it gets hot in the afternoon. Sisko joins the other men in the field, but the opening of a metal box takes their attention away from their work.

A young man named Stephen emerges from the box, barely alive, having been put there the day before for stealing a candle. Alixus insists that such methods of punishment are effective and were approved by the entire community, including Stephen. That night, a colonist named Cassandra attempts to seduce Sisko. When confronted about it, Alixus admits that she sent Cassandra but attempts to rationalize her behavior, which Sisko calls contemptible. She then assigns him to stand watch the rest of the night.

The next day, Alixus asks Sisko if he will be able to work his regular shift in the field. O'Brien objects, angrily noting that Sisko has just finished standing watch at her request, and she reassures Sisko that it is okay if he cannot work. However, Sisko insists on working his regular shift. Alixus suggests "some more comfortable clothes" for the task. Meanwhile, Kira and Dax discover Sisko and O'Brien's runabout aimlessly travelling at low warp.

Alixus informs the village that Meg has died and notes that no one was prouder of what the village has accomplished than she was, using this as a segue by which to announce that O'Brien has been discovered "defiling her memory." She announces that O'Brien was "wasting precious time" trying to activate his technological devices and, as his commanding officer, Sisko is placed in the punishment box. Once his punishment period is over, Alixus offers him water — if he will change out of his uniform. She leaves him alone with a change of clothes, but shortly thereafter he re-emerges still in his uniform. Sisko staggers toward the box and climbs inside once more.

Dax and Kira work on a way to find the runaway runabout's point of origin as O'Brien continues to work on a way to bypass the duonetic field. Joseph warns him but agrees to look the other way. O'Brien uses an improvised compass to locate the origin of the field, where he discovers a generator of some kind buried beneath the sand. Before O'Brien can investigate further, an arrow flies past his head. Vinod chases O'Brien, who manages to outsmart the younger man and brings him back to the village.

O'Brien opens the punishment box with his now-functional phaser and reveals to the colonists that the field was artificially created. However, when Sisko attempts to contact their runabout he finds it missing. Alixus emerges and admits that she destroyed the runabout and created the duonetic field, but she defends her actions by justifying them with the way in which each of the colonists has discovered potential they did not know they had. When Kira and Dax arrive, Sisko and O'Brien assume the colonists want to come with them, but Joseph intervenes:

"Miles, this is our home. Whatever Alixus may be guilty of, she did give us our community. I'm not sure if we'll leave the device on or off now that we know it's there. And we'll have to decide if we want to establish contact with the outside world. But Alixus is right: We have found something here that none of us is willing to give up."

"It's time for those of us who don't belong here to leave," Alixus says, and with that she, Vinod, O'Brien, and Sisko beam up. As the colonists go about their business, two young children are left staring at the point where the four vanished.